RC3.16.3

[jlgelpi]

New Release v3.16.3

[Copilot]

Pull request overview

Release bump to v3.16.3 for biobb_structure_checking, updating core structure-loading/analysis behavior (no-network caching, sequence mismatch reporting, summary metadata) and refreshing documentation plus test fixtures to match the new output.

Changes:

• Bump package/docs versioning to 3.16.3 and update changelogs.
• Extend runtime output/summary (e.g., include version tag; new sequence mismatch reporting; updated header/ligand/metal reporting).
• Refresh test harness + reference logs/JSON/FASTA fixtures to reflect updated output strings and behaviors.

Reviewed changes

Copilot reviewed 37 out of 105 changed files in this pull request and generated 8 comments.

Show a summary per file

File	Description
TODO	Update roadmap items / fix typo in modified-AA task line.
setup.py	Version bump + readme file opened with UTF-8 encoding.
README.md	Version string update.
CHANGELOG.md	Add v3.16.3 release notes + adjust prior entries.
biobb_structure_checking/test/scripts/test.sh	Adjust log normalization patterns for new download message text.
biobb_structure_checking/test/ref/load_cache.log	New reference output for cached-loading scenarios.
biobb_structure_checking/test/ref/6m0j_amide_test_auto.log	Update expected output strings (entry id/version).
biobb_structure_checking/test/ref/4mdh_cistransbck_test.log	Update expected output strings + modified residue labels.
biobb_structure_checking/test/ref/4ku1_getss_test.log	Update expected output strings (entry id/version).
biobb_structure_checking/test/ref/4ku1_getss_mark_test.log	Update expected output strings (entry id/version).
biobb_structure_checking/test/ref/4ku1_all_test.log	Update expected output strings and remove stray printed boolean lines.
biobb_structure_checking/test/ref/4ku1_all_test.json	Update expected JSON casing + include version tag.
biobb_structure_checking/test/ref/3nir_sequences.fasta	New reference FASTA output for sequence mismatch case.
biobb_structure_checking/test/ref/3nir_sequences_test.log	New reference log for sequence mismatch reporting.
biobb_structure_checking/test/ref/2ki5_sequences_test.log	Update expected output strings (entry id/version).
biobb_structure_checking/test/ref/2ki5_remwat_test_Yes.log	Update expected output strings (entry id/version).
biobb_structure_checking/test/ref/2ki5_remwat_test_None.log	Update expected output strings (entry id/version).
biobb_structure_checking/test/ref/2ki5_mutateside_test.log	Update expected output strings and remove stray printed boolean lines.
biobb_structure_checking/test/ref/2ki5_mutateside_test.json	Include version tag in expected JSON.
biobb_structure_checking/test/ref/2ki5_mutateside_rb_test.log	Update expected output strings (incl. environment/time) + remove stray printed boolean lines.
biobb_structure_checking/test/ref/2ki5_mutateside_rb_test.json	Include version tag in expected JSON.
biobb_structure_checking/test/ref/2ki5_ligands_test_SO4.log	Update expected output strings (entry id/version).
biobb_structure_checking/test/ref/2ki5_ligands_test_None.log	Update expected output strings (entry id/version).
biobb_structure_checking/test/ref/2ki5_ligands_test_All.log	Update expected output strings (entry id/version).
biobb_structure_checking/test/ref/2ki5_keepwat_test_3.log	Update expected output strings (entry id/version).
biobb_structure_checking/test/ref/2ki5_fixside_None_test.log	Update expected output strings (entry id/version).
biobb_structure_checking/test/ref/2ki5_fixside_All_test.log	Update expected output strings and remove stray printed boolean lines.
biobb_structure_checking/test/ref/2ki5_fixside_All_rb_test.log	Update expected output strings (incl. environment/time) + remove stray printed boolean lines.
biobb_structure_checking/test/ref/2ki5_clashes_test.log	Update expected output strings and remove stray printed boolean lines.
biobb_structure_checking/test/ref/2ki5_checkall_test.log	Update expected output strings and remove stray printed boolean lines.
biobb_structure_checking/test/ref/2ki5_chains_test_renum_chain.log	Update expected output strings (entry id/version).
biobb_structure_checking/test/ref/2ki5_chains_test_rebuild.log	Update expected output strings (entry id/version).
biobb_structure_checking/test/ref/2ki5_chains_test_fix_chains.log	Update expected output strings (entry id/version).
biobb_structure_checking/test/ref/2ki5_chains_test_B.log	Update expected output strings (entry id/version).
biobb_structure_checking/test/ref/2ki5_chains_test_all.log	Update expected output strings (entry id/version).
biobb_structure_checking/test/ref/2ki5_backbone_test.log	Update expected output strings (entry id/version).
biobb_structure_checking/test/ref/2ki5_altloc_test_occ.log	Update expected output strings (entry id/version).
biobb_structure_checking/test/ref/2ki5_altloc_test_B.log	Update expected output strings (entry id/version).
biobb_structure_checking/test/ref/2ki5_all_test.log	Update expected output strings and remove stray printed boolean lines.
biobb_structure_checking/test/ref/2ki5_all_test.json	Update expected JSON casing + include version tag.
biobb_structure_checking/test/ref/1vtk_checkall_test.log	Update expected output; metals detection output changed.
biobb_structure_checking/test/ref/1vtk_1_svc_all_test.log	Update expected output; metals detection output changed.
biobb_structure_checking/test/ref/1vtk_1_models_complex.log	Update expected output strings (entry id/version).
biobb_structure_checking/test/ref/1vtk_1_all_test.json	Update expected JSON for metals options + include version tag.
biobb_structure_checking/test/ref/1ubq_chi_none_test_None.log	Update expected output strings (entry id/version).
biobb_structure_checking/test/ref/1ubq_chi_chiral_test_All.log	Update expected output strings + remove stray printed boolean lines.
biobb_structure_checking/test/ref/1ubq_backbone_main_test.log	Update expected output strings (entry id/version) + environment/time.
biobb_structure_checking/test/ref/1ubq_backbone_caps_test.log	Update expected output strings + remove stray printed boolean lines.
biobb_structure_checking/test/ref/1ubq_amide_test_None.log	Update expected output strings (entry id/version).
biobb_structure_checking/test/ref/1ubq_amide_test_All.log	Update expected output strings (entry id/version).
biobb_structure_checking/test/ref/1ubq_all_test.log	Update expected output strings + remove stray printed boolean lines.
biobb_structure_checking/test/ref/1ubq_all_test.json	Include version tag in expected JSON.
biobb_structure_checking/test/ref/1ubq_all_test_debug.log	Update expected output (timings/memory/version strings).
biobb_structure_checking/test/ref/1ubq_all_test_debug.json	Update expected JSON timings/memory + include version tag.
biobb_structure_checking/test/ref/1ubq_add_hydrogen_PQR_test.log	Update expected output strings (entry id/version).
biobb_structure_checking/test/ref/1ubq_add_hydrogen_CMIP_test.log	Update expected output strings (entry id/version).
biobb_structure_checking/test/ref/1ubq_add_hydrogen_ADT_test.log	Update expected output strings (entry id/version).
biobb_structure_checking/test/ref/1svc_checkall_test.log	Update expected output strings + remove stray printed boolean lines.
biobb_structure_checking/test/ref/1svc_chains_test_rebuild.log	Update expected output strings (entry id/version).
biobb_structure_checking/test/ref/1svc_chains_test_protein.log	Update expected output strings (entry id/version).
biobb_structure_checking/test/ref/1svc_all_test.log	Update expected output strings + remove stray printed boolean lines.
biobb_structure_checking/test/ref/1svc_all_test.json	Include version tag in expected JSON.
biobb_structure_checking/test/ref/1rna_add_hydrogen_ADT_test.log	Update expected output strings (entry id/version).
biobb_structure_checking/test/ref/1ldn1_checkall_test.log	Update expected output strings + new microheterogeneity warning line.
biobb_structure_checking/test/ref/1d23_poliA_test.log	Update expected output strings + remove stray printed boolean lines.
biobb_structure_checking/test/ref/1d23_fixtest_All_test.log	Update expected output strings + remove stray printed boolean lines.
biobb_structure_checking/test/ref/1d23_dnamut_test.log	Update expected output strings + remove stray printed boolean lines.
biobb_structure_checking/test/ref/1d23_add_hydrogen_CMIP_test.log	Update expected output strings (entry id/version).
biobb_structure_checking/test/ref/1bqo_metals_test_ZN.log	Update expected output strings + truncated ligand label text.
biobb_structure_checking/test/ref/1bqo_metals_test_None.log	Update expected output strings + truncated ligand label text.
biobb_structure_checking/test/ref/1bqo_metals_test_All.log	Update expected output strings + truncated ligand label text.
biobb_structure_checking/test/ref/1bqo_metals_test_A305.log	Update expected output strings + truncated ligand label text.
biobb_structure_checking/test/ref/1bqo_all_test.log	Update expected output strings + remove stray printed boolean lines.
biobb_structure_checking/test/ref/1bqo_all_test.json	Include version tag in expected JSON.
biobb_structure_checking/test/ref/1ark_remh_test_Yes.log	Update expected output strings (entry id/version/model type label).
biobb_structure_checking/test/ref/1ark_remh_test_None.log	Update expected output strings (entry id/version/model type label).
biobb_structure_checking/test/ref/1ark_models_test_5.log	Update expected output strings (entry id/version/model type label).
biobb_structure_checking/test/ref/1ark_models_test_1.log	Update expected output strings (entry id/version/model type label).
biobb_structure_checking/test/ref/1ark_models_3-6_sup_test.log	Update expected output strings (entry id/version/model type label).
biobb_structure_checking/test/ref/1ark_chiral_bck_test.log	Update expected output strings (entry id/version).
biobb_structure_checking/test/ref/1ark_all_test.log	Update expected output strings + remove stray printed boolean lines.
biobb_structure_checking/test/ref/1ark_all_test.json	Include version tag in expected JSON.
biobb_structure_checking/test/ref/104l_inscodes_test.log	Update expected output strings (entry id/version).
biobb_structure_checking/test/ref/104l_inscodes_renum_test.log	Update expected output strings (entry id/version).
biobb_structure_checking/test/Makefile	Add sequences test target for 3nir.
biobb_structure_checking/structure_manager.py	No-network cached fetch path; encoding fixes; clash adjacency improvements; exception docstrings.
biobb_structure_checking/structure_checking.py	Initialize summary with version; safer exception messages; UTF-8 command list loading; remove stray debug print.
biobb_structure_checking/pdbio/param_input.py	Robust prompt building (string conversion/defaults).
biobb_structure_checking/pdbio/mmb_server.py	Adjust supported remote formats + download messaging cleanup.
biobb_structure_checking/mutation_manager.py	Simplify mutation string formatting.
biobb_structure_checking/modelling/utils.py	Update model labels; adjacency-aware clash logic; improved metal atom detection.
biobb_structure_checking/modelling/structuredata.py	Header printing changes + refactor HETATM stats printing.
biobb_structure_checking/modelling/sequencedata.py	Import cleanup + new canonical/structure mismatch comparison helper.
biobb_structure_checking/modelling/residue_set.py	Minor refactor + metadata field adjustments.
biobb_structure_checking/modelling/modelsdata.py	Formatting tweaks + include P atoms for model superposition.
biobb_structure_checking/docs/source/readme.md	Version string update.
biobb_structure_checking/docs/source/conf.py	Sphinx version/release bump.
biobb_structure_checking/docs/source/changelog.md	Add v3.16.3 notes.
biobb_structure_checking/constants.py	Version bump + message additions + UTF-8 help reading + wording updates.
biobb_structure_checking/commands/sequences.py	Print/emit sequence mismatch summary.
biobb_structure_checking/commands/chains.py	Small option parsing cleanup.
biobb_structure_checking/commands/backbone.py	Print modified residue labels when network is available.
biobb_structure_checking/commands/altloc.py	Add microheterogeneity warning + support “no selection” flow.
biobb_structure_checking/commands/add_hydrogen.py	Ensure pH is treated numerically + summary initialization fix.
biobb_structure_checking/check_structure.py	UTF-8 help text reading.

Suppressed comments (2)

CHANGELOG.md:14

• Grammar in release notes: "fields where missing" should be "fields were missing".

  - Fixed errors when required fields where missing from cif files 

biobb_structure_checking/docs/source/changelog.md:14

• Grammar in documentation changelog: "fields where missing" should be "fields were missing".

  - Fixed errors when required fields where missing from cif files 

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